Step 1: difcover

Step 2: SNPdensity

Female Reference Genome

Male Reference Genome

Step 2: GWAS & Fst

Female Reference Genome

PCA

All individuals

##  [1]   5.554972  11.049963  16.493342  21.834145  27.027838  32.101151
##  [7]  37.155872  42.182614  47.156312  52.104758  57.029665  61.904487
## [13]  66.748277  71.564689  76.345953  81.108673  85.862467  90.585923
## [19]  95.302720 100.000000
## [1] "full dataset - female ref"

## [1] "full dataset - female ref - zoom"

## [1] "full dataset - female ref"
## quartz_off_screen 
##                 2
# grab outliers
pca_outliers_f <- pca_f %>% filter(PC1 > 0.25 | PC2 < -0.1 | PC2 > 0.25)
print(pca_outliers_f$ind)
## [1] "RX41_2_M_F11_AAGGACAC.sort-n.fixmate-m.sort.markdup-r"
## [2] "RX47_1_F_G08_ATAGCGAC.sort-n.fixmate-m.sort.markdup-r"
## [3] "RX59_2_M_H11_GATGAATC.sort-n.fixmate-m.sort.markdup-r"
## [4] "RX68_2_M_G12_CACCTTAC.sort-n.fixmate-m.sort.markdup-r"
No Outliers

##  [1]   5.346634  10.560970  15.757442  20.890464  26.003575  31.102359
##  [7]  36.170534  41.207914  46.224175  51.221735  56.191477  61.135634
## [13]  66.053229  70.953426  75.831527  80.700464  85.564656  90.389354
## [19]  95.199957 100.000000
## [1] "no outliers - female ref"

## [1] "no outliers - female ref - zoom"

## [1] "no outliers - female ref"

## [1] "female ref\n row1=full dataset, row2=filtered"
## quartz_off_screen 
##                 2

GWAS

All Individuals
No Outliers

Fst

All Individuals
## [1] 0.0737052
## [1] 0.243856
## 
##         lg01         lg02         lg03         lg04         lg05         lg06 
##           83           90          108           82           51           89 
##         lg07         lg08         lg09         lg10         lg11         lg12 
##           79           99          129           96          145           89 
##         lg13         lg14         lg15         lg16         lg17         lg18 
##           91          141           98           32           98           95 
##         lg19         lg20         lg21         lg22         lg23         lg24 
##          118           39           59          106          138           38 
##         lg25         lg26 scaffold_101 scaffold_105 scaffold_107 scaffold_111 
##           37           63            1            3            5            3 
## scaffold_116 scaffold_122 scaffold_124 scaffold_127 scaffold_129 scaffold_130 
##            4            3            8            3            4            3 
## scaffold_131 scaffold_132 scaffold_133 scaffold_134 scaffold_137 scaffold_138 
##            1            6           20            3            2            2 
## scaffold_139 scaffold_143 scaffold_146 scaffold_149 scaffold_152 scaffold_154 
##            4            1            6            3            7            1 
## scaffold_156 scaffold_159 scaffold_160 scaffold_166 scaffold_170 scaffold_172 
##            4            2           10            5            6            1 
## scaffold_181 scaffold_184 scaffold_185 scaffold_186 scaffold_187 scaffold_192 
##            1            2            1            2            1            1 
## scaffold_194 scaffold_195 scaffold_199 scaffold_201 scaffold_203 scaffold_204 
##            5            3            2            1            3            1 
## scaffold_205 scaffold_208 scaffold_210 scaffold_214 scaffold_218 scaffold_221 
##            1            2            2            2            3            1 
## scaffold_223 scaffold_224 scaffold_225 scaffold_226 scaffold_227 scaffold_228 
##            3            1            3            1            1            3 
## scaffold_229 scaffold_231 scaffold_232 scaffold_234 scaffold_235 scaffold_236 
##            2            1            1            1            1            3 
## scaffold_241 scaffold_243 scaffold_250 scaffold_251 scaffold_256 scaffold_257 
##            2            4            4            2            2            1 
## scaffold_258 scaffold_260 scaffold_263 scaffold_264 scaffold_266  scaffold_27 
##            1            5            1            2            1           25 
## scaffold_270 scaffold_273 scaffold_276 scaffold_280 scaffold_284 scaffold_287 
##            1            1            1            2            1            1 
## scaffold_289 scaffold_290 scaffold_292 scaffold_293 scaffold_294 scaffold_295 
##            1            1            1            1            1            2 
## scaffold_296 scaffold_297  scaffold_30 scaffold_300 scaffold_306 scaffold_309 
##            1            3           24            2            1            1 
##  scaffold_31 scaffold_311 scaffold_312 scaffold_318 scaffold_321 scaffold_323 
##           28            1            3            1            1            1 
## scaffold_325 scaffold_326 scaffold_329 scaffold_330 scaffold_332 scaffold_333 
##            1            1            2            1            1            2 
## scaffold_335 scaffold_338 scaffold_339 scaffold_350 scaffold_353 scaffold_354 
##            2            3            1            1            2            1 
## scaffold_356 scaffold_369 scaffold_380 scaffold_381 scaffold_383 scaffold_386 
##            1            4            1            1            1            1 
## scaffold_389 scaffold_391 scaffold_409 scaffold_414  scaffold_42 scaffold_421 
##            2            1            1            1           20            2 
## scaffold_425 scaffold_426 scaffold_431 scaffold_434 scaffold_437 scaffold_438 
##            1            1            2            1            1            1 
## scaffold_443 scaffold_446 scaffold_450 scaffold_468 scaffold_472 scaffold_474 
##            2            1            1            1            1            1 
## scaffold_477 scaffold_478  scaffold_48 scaffold_480 scaffold_483 scaffold_491 
##            1            1            2            1            1            1 
## scaffold_495 scaffold_499 scaffold_503  scaffold_51 scaffold_512  scaffold_52 
##            1            1            1            1            1            4 
##  scaffold_55  scaffold_60  scaffold_61  scaffold_62  scaffold_64  scaffold_65 
##            2            1           11            5            3            4 
##  scaffold_84  scaffold_88  scaffold_89  scaffold_90  scaffold_91  scaffold_94 
##            8            2            4            1            1            1 
##  scaffold_96 
##            6
##       95%       99% 
## 0.0737052 0.2438305
## [1] 0.0182133

No Outliers
## [1] 0.118254
## [1] 0.193863
## 
##         lg01         lg02         lg03         lg04         lg05         lg06 
##            1            1            1            4            1            2 
##         lg07         lg08         lg09         lg10         lg11         lg12 
##            1            2            1            2            2            2 
##         lg13         lg14         lg15         lg16         lg17         lg18 
##            1            2            1            1            3            3 
##         lg19         lg20         lg21         lg22         lg23         lg26 
##            4            2            1            2            1            1 
## scaffold_204 scaffold_225 scaffold_263  scaffold_27 scaffold_297 scaffold_357 
##            1            1            1            1            1            1 
##  scaffold_42 
##            1
##      95%      99% 
## 0.117942 0.193146
## [1] 0.03776015

## [1] 0.118254
## [1] 0.193863
## 
##         lg01         lg02         lg03         lg04         lg05         lg06 
##            1            1            1            4            1            2 
##         lg07         lg08         lg09         lg10         lg11         lg12 
##            1            2            1            2            2            2 
##         lg13         lg14         lg15         lg16         lg17         lg18 
##            1            2            1            1            3            3 
##         lg19         lg20         lg21         lg22         lg23         lg26 
##            4            2            1            2            1            1 
## scaffold_204 scaffold_225 scaffold_263  scaffold_27 scaffold_297 scaffold_357 
##            1            1            1            1            1            1 
##  scaffold_42 
##            1
##      95%      99% 
## 0.117942 0.193146
## [1] 0.03776015

Male Reference Genome

PCA

All Individuals

##  [1]   5.608953  11.067687  16.446146  21.680707  26.857506  31.981802
##  [7]  37.071635  42.133003  47.140576  52.124343  57.057546  61.969341
## [13]  66.819038  71.647512  76.427544  81.172927  85.905439  90.617190
## [19]  95.315377 100.000000
## [1] "full dataset - male ref"

## [1] "full dataset - male ref - zoom"

## quartz_off_screen 
##                 2
# grab outliers
pca_outliers_m <- pca_m %>% filter(PC1 < -0.25 | PC2 < -0.25)
head(pca_outliers_m$ind)
## [1] "RX41_2_M_F11_AAGGACAC.sort-n.fixmate-m.sort.markdup-r"
## [2] "RX59_2_M_H11_GATGAATC.sort-n.fixmate-m.sort.markdup-r"
## [3] "RX68_2_M_G12_CACCTTAC.sort-n.fixmate-m.sort.markdup-r"
No Outliers

##  [1]   5.321484  10.552065  15.736116  20.897567  26.001281  31.085564
##  [7]  36.147891  41.190007  46.218987  51.209520  56.179934  61.125177
## [13]  66.067067  70.968994  75.845061  80.715432  85.570783  90.404499
## [19]  95.208129 100.000000
##  [1]   5.321484  10.552065  15.736116  20.897567  26.001281  31.085564
##  [7]  36.147891  41.190007  46.218987  51.209520  56.179934  61.125177
## [13]  66.067067  70.968994  75.845061  80.715432  85.570783  90.404499
## [19]  95.208129 100.000000
## [1] "No Outliers - MaleRef"

## [1] "No Outliers - MaleRef - Zoom"

## [1] "no outliers - female ref"

## [1] "male ref\n row1=full dataset, row2=filtered"
## quartz_off_screen 
##                 2

GWAS

All Individuals
No Outlier

Fst

All Individuals
## [1] 0.074878
## [1] 0.248619
## 
##         lg01         lg02         lg03         lg04         lg05         lg06 
##           95           70          126           86           73          107 
##         lg07         lg08         lg09         lg10         lg11         lg12 
##           68          101          106           59          118           76 
##         lg13         lg14         lg15         lg16         lg17         lg18 
##           73          120           67           32           61           93 
##         lg19         lg20         lg21         lg22         lg23         lg24 
##          102           43           53           95          112           14 
##         lg25         lg26 scaffold_106 scaffold_107 scaffold_111 scaffold_113 
##           27           57            2            3            1            8 
## scaffold_122 scaffold_129 scaffold_133 scaffold_134 scaffold_136 scaffold_137 
##            3            2            1            3            1            1 
## scaffold_138 scaffold_141 scaffold_142 scaffold_143 scaffold_145 scaffold_150 
##            2            3            2            4            1            1 
## scaffold_152 scaffold_154 scaffold_155 scaffold_156 scaffold_157 scaffold_166 
##            6            1            1            2            1            4 
## scaffold_169 scaffold_170 scaffold_171 scaffold_179 scaffold_182 scaffold_183 
##            4            4            3            2            7            2 
## scaffold_184 scaffold_185 scaffold_186 scaffold_194 scaffold_196  scaffold_20 
##            2            1            9            4            1           13 
## scaffold_202 scaffold_203 scaffold_204 scaffold_206 scaffold_207 scaffold_209 
##            1            1            3            2            1            1 
## scaffold_210 scaffold_212 scaffold_215 scaffold_222 scaffold_224 scaffold_227 
##            2            1            1            2            2            3 
## scaffold_228 scaffold_232 scaffold_233 scaffold_235 scaffold_236 scaffold_242 
##            1            3            1            2            4            5 
## scaffold_243 scaffold_248 scaffold_251 scaffold_256 scaffold_258 scaffold_260 
##            2            1            1            3            1            3 
## scaffold_262 scaffold_266  scaffold_28 scaffold_280 scaffold_282 scaffold_285 
##            3            1           16            4            2            1 
## scaffold_290 scaffold_291 scaffold_300 scaffold_301 scaffold_312 scaffold_321 
##            3            1            2            1            1            1 
## scaffold_322 scaffold_323 scaffold_324 scaffold_325 scaffold_330 scaffold_344 
##            2            1            1            1            1            1 
## scaffold_350 scaffold_353 scaffold_355 scaffold_357 scaffold_359 scaffold_364 
##            1            2            4            4            2            1 
## scaffold_365 scaffold_368 scaffold_370 scaffold_371 scaffold_374 scaffold_380 
##            1            1            1            1            2            2 
## scaffold_386 scaffold_413 scaffold_427 scaffold_429 scaffold_435 scaffold_441 
##            5            2            2            1            3            2 
## scaffold_444  scaffold_45 scaffold_451 scaffold_457 scaffold_458 scaffold_462 
##            1            3            2            1            2            1 
## scaffold_465 scaffold_467 scaffold_470 scaffold_479  scaffold_49 scaffold_493 
##            1            1            4            2            5            3 
## scaffold_495 scaffold_497 scaffold_498  scaffold_50 scaffold_511 scaffold_512 
##            2            1            3           13            2            2 
##  scaffold_54 scaffold_547 scaffold_548 scaffold_552 scaffold_554 scaffold_557 
##            2            1            1            2            1            1 
##  scaffold_57 scaffold_573 scaffold_579 scaffold_584 scaffold_595 scaffold_601 
##            3            1            1            1            1            2 
## scaffold_609  scaffold_61 scaffold_613 scaffold_616 scaffold_617 scaffold_622 
##            2            2            1            2            1            2 
## scaffold_623 scaffold_634 scaffold_637 scaffold_638 scaffold_639 scaffold_643 
##            1            1            1            1            2            1 
## scaffold_653 scaffold_661 scaffold_663 scaffold_670 scaffold_671 scaffold_674 
##            3            1            2            1            1            1 
## scaffold_676  scaffold_68 scaffold_680 scaffold_683 scaffold_685 scaffold_686 
##            1            6            1            1            2            1 
## scaffold_690 scaffold_693 scaffold_695 scaffold_705  scaffold_77  scaffold_81 
##            1            1            2            1            3            3 
##  scaffold_82  scaffold_85  scaffold_89   scaffold_9  scaffold_90  scaffold_92 
##            1            3            1           70            5            2 
##  scaffold_98 
##            2
##      95%      99% 
## 0.074878 0.248619
## [1] 0.01838211

No Outlier
## [1] 0.120286
## [1] 0.186137
## 
##         lg01         lg02         lg03         lg04         lg05         lg06 
##            2            1            1            5            1            3 
##         lg08         lg09         lg10         lg11         lg12         lg15 
##            1            1            4            1            3            1 
##         lg17         lg18         lg19         lg20         lg21         lg22 
##            1            2            4            1            1            1 
##         lg24         lg26 scaffold_184  scaffold_20 scaffold_206 scaffold_226 
##            1            3            1            1            1            1 
## scaffold_243 scaffold_458 scaffold_622 scaffold_682 
##            1            1            1            1
##       95%       99% 
## 0.1201978 0.1835650
## [1] 0.03747152

## [1] 0.120286
## [1] 0.186137
## 
##         lg01         lg02         lg03         lg04         lg05         lg06 
##            2            1            1            5            1            3 
##         lg08         lg09         lg10         lg11         lg12         lg15 
##            1            1            4            1            3            1 
##         lg17         lg18         lg19         lg20         lg21         lg22 
##            1            2            4            1            1            1 
##         lg24         lg26 scaffold_184  scaffold_20 scaffold_206 scaffold_226 
##            1            3            1            1            1            1 
## scaffold_243 scaffold_458 scaffold_622 scaffold_682 
##            1            1            1            1
##       95%       99% 
## 0.1201978 0.1835650
## [1] 0.03747152

Step 2: kmersgwas

All Individuals

No Outliers